How to "combine" two images for CNN input (classification task)?
You can combine the image output using concatenation. Please refer to this paper:

http://ivpl.eecs.northwestern.edu/sites/default/files/07444187.pdf

You can have a look at the Figure 2. And if you are using caffe, there is a layer called Concat layer. You can use it for your purpose.

I am not fully clear about what you want to do. But like you said, if you want to pass the image values from the first layer to some layers. Try reading about skip architectures.

If you want to use this network as real/fake finder, you can take the difference between two images and convert it to classification problem.

Hope it helps.